Virtually all forms of life exhibit the ability to control gene expression, e.g., in response to environmental conditions or as part of the developmental process, and a myriad of different mechanisms for controlling gene expression exist in nature. These mechanisms permit cells to express particular subsets of genes and allow them to adjust the level of particular gene products as required. For example, bacteria and eukaryotic cells are often able to adjust the expression of enzymes in synthetic or metabolic pathways depending on the availability of substrates or end products. Similarly, many cells are able to induce synthesis of protective molecules such as heat shock proteins in response to environmental stress. Inherited or acquired defects in mechanisms for control of gene expression are believed to play a significant role in human diseases (e.g., cancer), and targeted disruption of important regulatory molecules in mice frequently results in severe phenotypic defects.
A number of approaches have been developed in order to artificially control levels of gene expression, many of which are modeled on naturally occurring regulatory systems. In general, gene expression can be controlled at the level of RNA transcription or post-transcriptionally, e.g., by controlling the processing or degradation of mRNA molecules, or by controlling their translation. For example, modulating the activity of transcription factors (e.g., by administration of small molecule activators or inhibitors) is being pursued as a method of controlling mRNA levels (see, e.g., Nyanguile O, Uesugi M, Austin D J, Verdine G L. Proc Natl Acad Sci USA. 1997, 94(25):13402-6. A non-natural transcriptional coactivator.). Antisense strategies for gene silencing, in which an antisense RNA or DNA binds to a target RNA and results in inactivation, are also being actively pursued for applications ranging from functional genomics to therapeutics (Giles R V, “Antisense oligonucleotide technology: from EST to therapeutics” Curr Opin Mol Ther. 2000, 2(3):238-52). Nucleic acid enzymes such as ribozymes, i.e., RNA molecules that exhibit the ability to cleave other RNA molecules in a sequence-specific manner, offer another method for regulating gene expression (Sioud M., “Nucleic acid enzymes as a novel generation of anti-gene agents”, Curr Mol Med. 2001, 1(5):575-88). More recently, the discovery of RNA interference (RNAi), in which the presence of double-stranded RNA leads to degradation of a target RNA transcript, has provided another approach to the control of gene expression (Hutvagner, G. and Zamore, P D., “RNAi: nature abhors a double-strand”, Curr. Op. Genet. Dev., 12:225-232, 2002).
Although the approaches described above have proven extremely valuable, they have a variety of features that limit their usefulness. For example, methods that involve alterations in RNA transcription may have slower response times than methods that are based on post-transcriptional regulation. Techniques involving modulation of transcription factors are generally limited to well-characterized transcription factors. Antisense, ribozyme, and RNAi-based approaches typically require sequence-specific design. It is evident that a need exists in the art for additional systems and methods for the control of gene expression. In particular, there exists a need for modular systems that function with a wide variety of genes and that can be integrated into biological networks. Furthermore, there exists a need in the art for systems that would afford the ability to artificially control gene expression within cells in response to external stimuli.